Contacts of the helix formed by residues 56 - 65 (chain I) in PDB entry 3LUE
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 56 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54I VAL 3.4 2.5 + - - +
55I GLY* 1.3 68.9 - - - -
57I GLU* 1.3 63.2 + - - +
58I ALA 2.9 5.4 - - - -
59I GLN* 2.9 27.1 + - + +
60I SER* 3.1 20.0 + - - +
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Residues in contact with GLU 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I LYS* 3.6 5.9 + - - -
53I TYR* 3.6 22.2 - - + +
54I VAL 3.3 23.6 + - - +
56I ASP* 1.3 81.5 + - - +
58I ALA* 1.3 56.1 + - - +
60I SER* 4.4 8.3 - - - +
61I LYS* 4.3 19.1 + - - +
127R GLU* 5.1 3.1 - - - +
128R GLU* 2.7 36.5 - - - +
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Residues in contact with ALA 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I ILE* 4.9 2.5 - - - +
36I GLY 4.5 0.7 - - - +
53I TYR* 3.6 35.7 - - + +
54I VAL 4.0 1.8 - - - +
55I GLY 3.5 12.5 + - - +
56I ASP 2.9 0.8 - - - -
57I GLU* 1.3 77.8 - - - +
59I GLN* 1.3 66.3 + - - +
60I SER 3.3 0.9 - - - -
61I LYS 3.9 3.2 - - - +
62I ARG* 3.3 19.6 + - - +
65I LEU* 4.4 8.6 - - + +
67I LEU* 3.7 22.8 - - + +
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Residues in contact with GLN 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I SER 5.1 7.1 - - - +
34I ILE* 4.4 12.3 - - + +
55I GLY 3.5 4.5 + - - +
56I ASP* 2.9 23.0 + - + +
58I ALA* 1.3 80.1 - - - +
60I SER* 1.3 59.6 + - - +
61I LYS 2.9 0.4 + - - -
62I ARG* 2.8 69.7 + - - +
67I LEU* 5.4 0.2 - - - +
70I PRO* 5.8 2.9 - - - +
203I THR* 3.4 15.0 - - + +
204I ALA* 5.2 9.9 - - - -
207I GLU* 4.9 16.2 - - + +
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Residues in contact with SER 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56I ASP* 3.1 15.2 + - - +
57I GLU* 5.1 4.5 - - - -
58I ALA 3.3 0.6 - - - -
59I GLN* 1.3 74.5 - - - +
61I LYS* 1.3 70.1 + - - +
202I THR* 5.8 4.8 - - - +
203I THR* 4.1 16.9 + - - -
204I ALA* 3.6 28.6 - - - +
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Residues in contact with LYS 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I MET* 5.3 7.8 - - - +
47I MET* 4.5 22.3 - - - +
53I TYR* 4.4 24.9 - - + -
57I GLU* 4.3 20.6 + - - +
58I ALA 3.9 2.2 + - - +
59I GLN 2.9 0.6 + - - -
60I SER* 1.3 86.2 + - - +
62I ARG* 1.4 55.8 + - - +
63I GLY 3.2 2.9 - - - -
64I ILE* 2.8 51.2 + - + +
65I LEU* 2.9 28.2 + - + +
203I THR* 4.7 1.8 + - - -
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Residues in contact with ARG 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I ILE* 4.8 4.2 - - - +
58I ALA 3.3 13.6 + - - +
59I GLN* 2.8 52.9 + - - +
61I LYS* 1.4 72.9 - - - +
63I GLY* 1.3 62.6 + - - +
65I LEU* 2.9 27.2 - - - +
67I LEU* 3.9 29.4 - - + +
69I TYR* 3.9 15.5 + - - -
70I PRO* 4.9 14.0 - - - +
77I THR* 5.7 1.4 + - - -
78I ASN* 4.4 25.5 - - - +
81I ASP* 5.4 0.2 - - - -
203I THR* 4.2 14.5 - - + +
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Residues in contact with GLY 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61I LYS 3.2 0.8 - - - -
62I ARG* 1.3 84.2 - - - +
64I ILE* 1.3 60.0 + - - +
65I LEU 3.6 1.0 + - - +
203I THR* 4.9 6.3 + - - +
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Residues in contact with ILE 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I PRO 4.1 9.4 - - - +
61I LYS* 2.8 55.7 + - + +
63I GLY* 1.3 73.8 - - - -
65I LEU* 1.4 63.7 + - + +
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Residues in contact with LEU 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36I GLY* 3.9 16.2 - - - +
37I ARG 4.2 2.9 - - - +
38I PRO* 3.6 38.6 - - + -
39I ARG* 5.7 0.4 - - - -
53I TYR* 3.8 29.8 - - + -
58I ALA* 4.4 9.9 - - + +
61I LYS* 2.9 40.6 + - + +
62I ARG* 2.9 19.1 + - - +
63I GLY 3.4 1.4 + - - +
64I ILE* 1.4 90.1 - - + +
66I THR* 1.3 64.8 + - - +
67I LEU* 3.8 5.4 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il